Target folder: C:/Git/ETN_workshop_Jan2021/actel_example
Timestamp: 2021-01-25 15:31:21
Number of target tags: 60
Number of listed receivers: 17 (of which 1 had no detections)
Data time range: 2018-04-13 22:26:37 to 2018-05-25 17:46:13 (Europe/Copenhagen).
Percentage of post-release valid detections: 100%
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Arrays with the same background belong to the same section. Release sites are marked with “R.S.”. Arrays connected with an arrow indicate that the animals can only pass in one direction.
| Station.name | Latitude | Longitude | x | y | Array | Section | Standard.name |
|---|---|---|---|---|---|---|---|
| Station -1 | 56.35474 | 8.629019 | 477075.2 | 6245625 | A0 | River | St.1 |
| Station 1 | 56.35672 | 8.603097 | 475474.6 | 6245854 | A1 | River | St.2 |
| Station 2 | 56.36505 | 8.510094 | 469734.4 | 6246818 | A2 | River | St.3 |
| Station 3 | 56.34976 | 8.385683 | 462033.4 | 6245178 | A3 | River | St.4 |
| Station 4 | 56.32894 | 8.309133 | 457279.2 | 6242906 | A4 | River | St.5 |
| Station 5 | 56.32576 | 8.306444 | 457109.4 | 6242553 | A5 | River | St.6 |
| Station 6 | 56.32267 | 8.303267 | 456909.4 | 6242211 | A6 | River | St.7 |
| Station 7 | 56.32865 | 8.249125 | 453568.3 | 6242912 | A7 | Fjord | St.8 |
| Station 8 | 56.32610 | 8.246447 | 453399.6 | 6242630 | A7 | Fjord | St.9 |
| Station 9 | 56.32388 | 8.240797 | 453047.5 | 6242387 | A7 | Fjord | St.10 |
| Station 10 | 56.32192 | 8.239672 | 452975.5 | 6242169 | A7 | Fjord | St.11 |
| Station 11 | 56.37173 | 8.132342 | 446407.4 | 6247792 | A8 | Fjord | St.12 |
| Station 12 | 56.37221 | 8.130017 | 446264.5 | 6247847 | A8 | Fjord | St.13 |
| Station 13 | 56.37250 | 8.127761 | 446125.6 | 6247881 | A8 | Fjord | St.14 |
| Station 14 | 56.37199 | 8.118439 | 445549.1 | 6247831 | A9 | Sea | St.15 |
| Station 15 | 56.37256 | 8.118169 | 445533.2 | 6247895 | A9 | Sea | St.16 |
| Station 16 | 56.37200 | 8.117658 | 445500.9 | 6247833 | A9 | Sea | St.17 |
| Receiver | Array | Station.name | Standard.name | Start | Stop |
|---|---|---|---|---|---|
| 132907 | A0 | Station -1 | St.1 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 132908 | A1 | Station 1 | St.2 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 132909 | A7 | Station 7 | St.8 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 132914 | A5 | Station 5 | St.6 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 132915 | A6 | Station 6 | St.7 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 132916 | A4 | Station 4 | St.5 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 132917 | A3 | Station 3 | St.4 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 132918 | A2 | Station 2 | St.3 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133205 | A8 | Station 13 | St.14 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133206 | A9 | Station 16 | St.17 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133209 | A8 | Station 12 | St.13 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133210 | A9 | Station 14 | St.15 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133215 | A9 | Station 15 | St.16 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133220 | A8 | Station 11 | St.12 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133221 | A7 | Station 10 | St.11 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133222 | A7 | Station 8 | St.9 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| 133224 | A7 | Station 9 | St.10 | 2018-03-15 12:00:00 | 2018-06-01 12:00:00 |
| Station.name | Latitude | Longitude | x | y | Array | Type | Standard.name | n.A | n.B |
|---|---|---|---|---|---|---|---|---|---|
| RS1 | 56.349 | 8.6204 | 476539 | 6244988 | A1 | Release | RS1 | 30 | 30 |
overall.CJS object. Auxiliary information can also be found in the matrices and arrays objects.
advEfficiency(results$overall.CJS) to obtain beta-drawn efficiency distributions (replace results with the name of the object where you saved the analysis).
Individuals detected and estimated
| A0 | A1 | A2 | A3 | A4 | A5 | A6 | A7 | A8 | A9 | |
|---|---|---|---|---|---|---|---|---|---|---|
| detected | 0 | 54 | 54 | 52 | 52 | 52 | 52 | 49 | 44 | 35 |
| here plus on peers | - | 54 | 54 | 50 | 52 | 52 | 50 | 43 | 35 | - |
| not here but on peers | - | 0 | 0 | 2 | 0 | 0 | 0 | 1 | 0 | - |
| known | 0 | 54 | 54 | 54 | 52 | 52 | 52 | 50 | 44 | 35 |
| estimated | - | 54 | 54 | 54 | 52 | 52 | 52 | 50 | 44 | - |
Array efficiency
Note: These values already include any intra-array efficiency estimates that have been requested.
| A0 | A1 | A2 | A3 | A4 | A5 | A6 | A7 | A8 | A9 | |
|---|---|---|---|---|---|---|---|---|---|---|
| efficiency | - | 100% | 100% | 96.2% | 100% | 100% | 100% | 97.7% | 100% | - |
Warning: GUI is set to 'needed' but packages 'gWidgets2', 'gWidgets2RGtk2', 'RGtk2' are not available. Please install them if you intend to run GUI.
Disabling GUI (i.e. GUI = 'never') for the current run.
Warning: No detections were found for receiver(s) 132907.
Warning: 'success.arrays' was not defined. Assuming success if the tags are last detected at array A9.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.
Warning: Inter-section backwards movements were detected for tag R64K-4508 (30/54).
Warning: Inter-section backwards movements were detected for tag R64K-4526 (45/54).
Warning: No tags passed through array A0. Skipping efficiency estimations for this array.
No comments were included during the analysis.
section.overview object.
| Total | Disap..in.River | Migrated.to.Fjord | Disap..in.Fjord | Migrated.to.Sea | Disap..in.Sea | Succeeded | |
|---|---|---|---|---|---|---|---|
| A | 30 | 4 | 26 | 1 | 25 | 5 | 20 |
| B | 30 | 4 | 26 | 7 | 19 | 4 | 15 |
status.df object (‘Very.last.array’ column).
Zoom in or open the figure in a new tab to clearly read the text within each circle.
overall.CJS object, and the data used in the tables is stored in the group.overview object. You can find detailed progressions per release site in the release.overview object.
Group: A
| Release | A0 | A1 | A2 | A3 | A4 | A5 | A6 | A7 | A8 | A9 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| detected | 30 | 0 | 26 | 26 | 25 | 26 | 26 | 26 | 26 | 25 | 20 |
| here plus on peers | - | - | 26 | 26 | 25 | 26 | 26 | 26 | 25 | 20 | - |
| not here but on peers | - | - | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | - |
| known | 30 | 0 | 26 | 26 | 26 | 26 | 26 | 26 | 26 | 25 | 20 |
| estimated | - | - | 26 | 26 | 26 | 26 | 26 | 26 | 26 | 25 | - |
| difference | - | - | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - |
Group: B
| Release | A0 | A1 | A2 | A3 | A4 | A5 | A6 | A7 | A8 | A9 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| detected | 30 | 0 | 28 | 28 | 27 | 26 | 26 | 26 | 23 | 19 | 15 |
| here plus on peers | - | - | 28 | 28 | 25 | 26 | 26 | 24 | 18 | 15 | - |
| not here but on peers | - | - | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | - |
| known | 30 | 0 | 28 | 28 | 28 | 26 | 26 | 26 | 24 | 19 | 15 |
| estimated | - | - | 28 | 28 | 28 | 26 | 26 | 26 | 24 | 19 | - |
| difference | - | - | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - |
plotTimes() function.
times object.
status.df object.
detections.y.axis argument.
section.order argument.
plotDetections() function.
plotMoves() function.
detections and movements objects (and respective valid counterparts).
detections.y.axis.
valid.detections object.
plotSensors() function.
Actel R package report.
Version: 1.2.1
Target folder: C:/Git/ETN_workshop_Jan2021/actel_example
Timestamp: 2021-01-25 15:31:21
Function: migration()
M: 'report' option has been activated.
M: Importing data. This process may take a while.
M: Number of target tags: 60.
M: Matching detections with deployment periods.
M: Number of ALS: 17 (of which 1 had no detections)
Warning: No detections were found for receiver(s) 132907.
M: Data time range: 2018-04-13 22:26:37 to 2018-05-25 17:46:13 (Europe/Copenhagen).
M: File 'distances.csv' found, activating speed calculations.
M: Data successfully imported!
Warning: 'success.arrays' was not defined. Assuming success if the tags are last detected at array A9.
M: Creating movement records for the valid tags.
M: Checking movement events quality.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.
M: Compiling and checking section movements for the valid tags.
Warning: Inter-section backwards movements were detected for tag R64K-4508 (30/54).
Warning: Inter-section backwards movements were detected for tag R64K-4526 (45/54).
M: Filtering valid array movements.
M: Filtering valid section movements.
M: Compiling migration timetable.
M: Compiling summary information tables.
Warning: No tags passed through array A0. Skipping efficiency estimations for this array.
M: Calculating array efficiency.
M: Saving results as 'actel_migration_results.RData'.
M: Producing the report.
M: Drawing individual detection graphics.
M: Printing sensor values for tags with sensor data.
M: Process finished successfully.
-------------------
User interventions:
-------------------
n # invalidate/expand moves in R64K-4508?
n # invalidate/expand moves in R64K-4526?
y # save results?
-------------------
Function call:
-------------------
migration(tz = 'Europe/Copenhagen', section.order = NULL, datapack = NULL, success.arrays = NULL, max.interval = 60, minimum.detections = 2, start.time = NULL, stop.time = NULL, speed.method = 'last to first', speed.warning = NULL, speed.error = NULL, jump.warning = 2, jump.error = 3, inactive.warning = NULL, inactive.error = NULL, exclude.tags = NULL, override = NULL, report = TRUE, auto.open = TRUE, discard.orphans = FALSE, discard.first = NULL, save.detections = FALSE, if.last.skip.section = TRUE, replicates = NULL, disregard.parallels = TRUE, GUI = 'never', save.tables.locally = FALSE, print.releases = TRUE, detections.y.axis = 'auto')
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